Variant report

Variant	rs10008773
Chromosome Location	chr4:106947203-106947204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:106947111-106947265	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000249635	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10000428	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10003024	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10004611	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10008428	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10016884	0.86[ASN][1000 genomes]
rs10017969	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10018910	0.88[ASN][1000 genomes]
rs10025052	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10027207	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10030019	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10049933	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11097912	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11732251	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11732791	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11931386	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11932523	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11942153	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12509366	0.82[EUR][1000 genomes]
rs12509640	0.81[EUR][1000 genomes]
rs12510966	0.83[EUR][1000 genomes]
rs12512683	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12513345	1.00[ASN][1000 genomes]
rs12642691	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12642900	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13101612	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13113845	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13114479	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13121614	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13138528	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17272618	0.88[ASN][1000 genomes]
rs28391259	0.82[EUR][1000 genomes]
rs28394440	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28467469	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28784652	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28805707	0.87[ASN][1000 genomes]
rs28822186	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs28845843	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28897193	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4306956	0.95[EUR][1000 genomes]
rs4307042	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4314353	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4355394	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4364267	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4374692	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4382109	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4470632	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4508971	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4569824	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4577583	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4600995	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55633564	0.83[EUR][1000 genomes]
rs60538413	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs62321365	0.82[EUR][1000 genomes]
rs6533237	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533242	0.82[EUR][1000 genomes]
rs6819081	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6823347	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6824682	0.82[EUR][1000 genomes]
rs6828362	0.83[EUR][1000 genomes]
rs6836198	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6842919	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6843331	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6844105	0.88[ASN][1000 genomes]
rs6846579	0.80[EUR][1000 genomes]
rs6849573	0.88[ASN][1000 genomes]
rs6852388	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6853554	1.00[ASN][1000 genomes]
rs72677306	0.83[EUR][1000 genomes]
rs7438546	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7657962	0.83[EUR][1000 genomes]
rs7662592	0.83[EUR][1000 genomes]
rs7667596	0.83[ASN][1000 genomes]
rs7668276	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7673101	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7677248	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7678847	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7682646	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7687657	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7689298	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7692069	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7693333	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7693448	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9685464	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9991091	0.84[EUR][1000 genomes]
rs9996093	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014993	chr4:106796019-106980727	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522792	chr4:106895964-106982793	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10008773	MGC16169	Cis_1M	lymphoblastoid	RTeQTL
rs10008773	SCYE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:1 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106935000-106948400	Weak transcription	Aorta	Aorta

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